8F7S: Gi bound delta-opioid receptor
Gi bound delta-opioid receptor in complex with deltorphin. Determined by electron microscopy at 3.0 Å resolution. Released 14 Dec 2022.
- Method
- Electron microscopy
- Resolution
- 3.0 Å
- Organisms
- Homo sapiens, Phyllomedusa, Rattus norvegicus
- Chains
- 8
- Atoms
- 9,975
- Mol. weight
- 219.35 kDa
- Ligands
- PLM, CLR
- Released
- 14 Dec 2022
Explore 8F7S in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8F7S contains 50 α-helices and 40 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 10 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-31 | 25 | |
| β-strand | 34-40 | 7 | 2 |
| α-helix | 46-54 | 9 | |
| β-strand | 185-190 | 6 | 2 |
| β-strand | 195-200 | 6 | 2 |
| α-helix | 208-211 | 4 | |
| α-helix | 212-216 | 5 | |
| β-strand | 220-226 | 7 | 2 |
| α-helix | 227-230 | 4 | |
| β-strand | 233 | 1 | 3 |
| β-strand | 241 | 1 | 3 |
| α-helix | 242-254 | 13 | |
| α-helix | 257-259 | 3 | |
| β-strand | 263-269 | 7 | 2 |
| α-helix | 271-280 | 10 | |
| α-helix | 296-308 | 13 | |
| β-strand | 319-323 | 5 | 2 |
| α-helix | 331-351 | 21 | |
Chain B: 5 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-30 | 22 | |
| α-helix | 35-38 | 4 | |
| α-helix | 39-41 | 3 | |
| α-helix | 43-44 | 2 | |
| β-strand | 52-56 | 5 | 4 |
| β-strand | 63-68 | 6 | 5 |
| β-strand | 74-79 | 6 | 5 |
| β-strand | 83-88 | 6 | 5 |
| β-strand | 93-99 | 7 | 5 |
| β-strand | 107-110 | 4 | 6 |
| β-strand | 116-120 | 5 | 6 |
| β-strand | 126-130 | 5 | 6 |
| β-strand | 139-144 | 6 | 6 |
| β-strand | 151-156 | 6 | 7 |
| β-strand | 161-166 | 6 | 7 |
| β-strand | 171-175 | 5 | 7 |
| β-strand | 180-185 | 6 | 7 |
| β-strand | 192-197 | 6 | 8 |
| β-strand | 203-208 | 6 | 8 |
| β-strand | 213-217 | 5 | 8 |
| β-strand | 223-227 | 5 | 8 |
| β-strand | 234-239 | 6 | 9 |
| β-strand | 245-250 | 6 | 9 |
| β-strand | 255-259 | 5 | 9 |
| β-strand | 264-269 | 6 | 9 |
| α-helix | 277 | 1 | |
| β-strand | 278-283 | 6 | 10 |
| β-strand | 289-294 | 6 | 10 |
| β-strand | 299-303 | 5 | 10 |
| β-strand | 309-313 | 5 | 10 |
| β-strand | 320-325 | 6 | 4 |
| β-strand | 332-336 | 5 | 4 |
| β-strand | 341-344 | 4 | 4 |
Chain C: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-23 | 16 | |
| α-helix | 27-29 | 3 | |
| α-helix | 30-43 | 14 | |
Chain D: 14 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-73 | 28 | |
| α-helix | 74-78 | 5 | |
| α-helix | 83-99 | 17 | |
| α-helix | 102-111 | 10 | |
| α-helix | 118-151 | 34 | |
| α-helix | 153-159 | 7 | |
| α-helix | 162-186 | 25 | |
| β-strand | 187-192 | 6 | 11 |
| β-strand | 195-200 | 6 | 11 |
| α-helix | 201-203 | 3 | |
| α-helix | 206-218 | 13 | |
| α-helix | 219-223 | 5 | |
| α-helix | 224-240 | 17 | |
| α-helix | 250-286 | 37 | |
| α-helix | 294-321 | 28 | |
| α-helix | 323-332 | 10 | |
Chain F: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 337-351 | 15 | |
Chains P and Q: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
Chain R: 15 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-73 | 28 | |
| α-helix | 74-78 | 5 | |
| α-helix | 83-99 | 17 | |
| α-helix | 102-111 | 10 | |
| α-helix | 118-151 | 34 | |
| α-helix | 153-159 | 7 | |
| α-helix | 162-186 | 25 | |
| β-strand | 187-192 | 6 | 1 |
| β-strand | 195-200 | 6 | 1 |
| α-helix | 203 | 1 | |
| α-helix | 206-218 | 13 | |
| α-helix | 219-223 | 5 | |
| α-helix | 224-240 | 17 | |
| α-helix | 244-246 | 3 | |
| α-helix | 250-286 | 37 | |
| α-helix | 294-321 | 28 | |
| α-helix | 323-332 | 10 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Delta-type opioid receptor | D, R | protein | 390 | Homo sapiens | P41143 (AlphaFold model) |
| deltorphin | P, Q | protein | 8 | Phyllomedusa | P21850 (AlphaFold model) |
| Guanine nucleotide-binding protein G(i) subunit alpha-1 | A, F | protein | 354 | Homo sapiens | P63096 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | B | protein | 353 | Rattus norvegicus | P54311 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | C | protein | 68 | Bos taurus | P63212 |
Sequence of entity 1 (D, R), FASTA
>8F7S_1 Delta-type opioid receptor (chains D, R)
DYKDDDDVDASEPAPSAGAELQPPLFANASDAYPSACPSAGANASGPPGARSASSLALAI
AITALYSAVCAVGLLGNVLVMFVIVRYTKMKTATNIYIFSLALAGALATSTLPFQSAKYL
METWPFGELLCKAVLSIDYYSMFTSIFTLTMMCVDRYIAVCHPVKALDFRTPAKAKLINI
CIWVLASGVGVPIMVMAVTRPRDGAVVCMLQFPSPSWYWDTVTKICVFLFAFVVPILIIT
VCYGLMLLRLRSVRLLSGSKEKDRSLRRITRMVLVVVVAFVVCWAPIHIFVIVWTLVDID
RRDPLVVAALHLCIALGYINSSLNPVLYAFLDENFKRCFRQLCRKPCGRPDPSSFSRARE
ATARERVTACTPSDGPGGGAAAHHHHHHHH
Sequence of entity 2 (P, Q), FASTA
>8F7S_2 deltorphin (chains P, Q)
YAFEVVGX
Sequence of entity 3 (A, F), FASTA
>8F7S_3 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A, F)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF
Sequence of entity 4 (B), FASTA
>8F7S_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRT
RRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAP
SGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCA
LWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHES
DINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLA
GYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN
Sequence of entity 5 (C), FASTA
>8F7S_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFC
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| PLM | Palmitic acid | C16 H32 O2 | 12 |
| CLR | Cholesterol | C27 H46 O | 5 |
Primary citation
Structures of the entire human opioid receptor family. Wang, Y., Zhuang, Y., DiBerto, J.F. et al. Cell (2023) 186:413-427.e17. DOI 10.1016/j.cell.2022.12.026 · PubMed
Other PDB entries of the same protein (UniProt P41143 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4N6H 1.8 Å, 1.8 A Structure of the human delta opioid 7TM receptor (PSI Community Target)
- 9YDP 1.95 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE
- 9CGK 2.62 Å, CryoEM structure of delta opioid receptor bound to G proteins and a full bitopic agonist
- 4RWD 2.7 Å, XFEL structure of the human delta opioid receptor in complex with a bifunctional peptide
- 9XDQ 2.79 Å, Cryo-EM structure of BMS986187 bound DOR-Gi complex
- 6PT2 2.8 Å, Crystal structure of the active delta opioid receptor in complex with the peptide…
- 9CGJ 2.8 Å, CryoEM structure of delta opioid receptor bound to G proteins and a partial agonist
- 8Y71 2.97 Å, positive allosteric modulator(BMS986187)-bound delta-opioid receptor-Gi complex
- 9PPX 3.04 Å, CryoEM structure of delta opioid receptor bound to G proteins and naltrexone
- 9XF4 3.05 Å, Cryo-EM structure of Leu-enkephalin-BMS-986187-bound DOR-Gi2 complex
- 9PPY 3.1 Å, CryoEM structure of delta opioid receptor bound to G proteins and met-enkephalin
- 9PQ0 3.12 Å, CryoEM structure of delta opioid receptor bound to G proteins and ADL5859
Browse structure collections
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